Search

By using core, logging curves, and experiment data, favorable lithofacies types in the 2nd Member of Triassic Xujiahe Formation in the Xinchang area, Sichuan Basin were classified, standard of the favorable lithofacies was established, planar distribution regularities of the favorable lithofacies were identified, and forming mechanisms of the favorable lithofacies and their control effect on production were examined. (1) The 2nd Member of Xujiahe Formation has twelve types of lithofacies, among which multiple layer medium-coarse grain sandstone lithofacies, parallel bedding medium-coarse grain sandstone lithofacies, massive bedding medium-coarse grain sandstone lithofacies, inclined bedding medium-coarse grain sandstone lithofacies, and charcoal-bearing medium-coarse grain sandstone lithofacies with better physical properties and higher gas content are favorable lithofacies; they feature low gamma, low neutron porosity, low resistivity, and high acoustic travel time on logging curves. (2) The sedimentary process controls spatial distribution of sand bodies which are the material basis of the favorable lithofacies; post diagenetic fluids would differentially reconstruct the favorable lithofacies; tectonic activities and abnormal formation pressure made strata slide along the weakness plane, giving rise to fractures in different types of rocks, which can enhance the reservoir permeability significantly. (3) The development degree of favorable lithofacies is a major factor affecting stable production of gas well.

Objectives To develop a sensitive monoclonal antibody-based sandwich enzyme-linked immunosorbent assay (ELISA) to detect Vip3Aa in genetically modified (GM) crops and their products. Results Vegetative insecticidal proteins (Vips) are secreted by Bacillus thuringiensis (Bt) and are known to be toxic to Lepidoptera species. Vip3Aa family proteins, Vip3Aa19 and Vip3Aa20, were successfully applied in GM crops to confer an effective and persistent insecticidal resistance. A sensitive monoclonal antibody-based sandwich ELISA was developed to detect Vip3Aa in GM crops and their products. Two monoclonal antibodies were raised against the overexpressed and purified His-Vip3Aa20, were purified from mouse ascites and characterized. A sandwich ELISA method was developed using the 2G3-1D7 monoclonal antibody for capture and the biotin-labeled 1F9-1F5 monoclonal antibody for detection of Vip3Aa20. The linear detection range of the method was found to be approximately 31.25–500 pg/ml, with a sensitivity of 10.24 pg/ml. Conclusions The established ELISA was effective for detecting Vip3Aa family proteins other than Vip3Aa8, and was successfully applied in the detection of Vip3Aa20 and Vip3Aa19 expressed in transgenic maize and cotton.

As a pathogenic bacterium, Bacillus thuringiensis (Bt) has become an alternative to chemical insecticides in commercial agricultural to control forestry pests and mosquitoes. To prevent pest resistance, many novel Bt strains have been isolated. Strain S3580-1 (WGS: VHPX0000000) used in this research and originally isolated from Hainan Qixianling National Forest Park (China) showed significant toxicity to Culex pipiens pallens. Here, using whole genome sequencing, assembly, and bioinformatics analysis, the predicted S3580-1CG_5163 (GenBank Accession No. MK124137) gene-encoded protein was found to share low homology with known toxins designated by the Bt toxin nomenclature system. It was considered to be an ETX/MTX2-type toxin and was designated Epp. Bioinformatics analysis showed that the predicted S3580-1CG_5163 gene-encoded protein Epp shared low identity with other known toxic protein sequences containing Cry-ETX/MTX conserved domains at the amino acid level, but significant similarity at the structural level. In addition, bioassays showed that Epp was toxic against Spodoptera litura (LC(50) 296.133 μg/mL; 95% FL 200.555–471.318 μg/mL) and Cx. pipiens pallens (LC(50) 322.193 μg/mL; 95% FL 238.217–477.243 μg/mL). On pathological observation, the peritrophic membrane of Cx. pipiens pallens larvae was degraded causing the midgut structure to become incomplete, resulting in larval death. Further bioassays are required to fully elucidate the insecticidal spectrum of the ETX/MTX2-type toxin Epp, and thereby provide future research directions.

Unintended effects of genetically modified (GM) crops may pose safety issues. Omics techniques provide researchers with useful tools to assess such unintended effects. Proteomics and metabolomics analyses were performed for three GM maize varieties, 2A-7, CC-2, and 2A-7×CC-2 stacked transgenic maize, and the corresponding non-GM parent Zheng58. Proteomics revealed 120, 271 and 135 maize differentially expressed proteins (DEPs) in the 2A-7/Zheng58, CC-2/Zheng58 and 2A-7×CC-2/Zheng58 comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEPs participated in metabolic pathways and the biosynthesis of secondary metabolite. Metabolomics revealed 179, 135 and 131 differentially accumulated metabolites (DAMs) in the 2A-7/Zheng58, CC-2/Zheng58 and 2A-7×CC-2/Zheng58 comparisons, respectively. Based on KEGG enrichment analysis, most DAMs are involved in the biosynthesis of secondary metabolite and metabolic pathways. According to integrated proteomics and metabolomics analysis, the introduction of exogenous EPSPS did not affect the expression levels of six other enzymes or the abundance of seven metabolites involved in the shikimic acid pathway in CC-2 and 2A-7×CC-2 seeds. Six co-DEPs annotated by integrated proteomics and metabolomics pathway analysis were further analyzed by qRT-PCR. This study successfully employed integrated proteomic and metabolomic technology to assess unintended changes in maize varieties. The results suggest that GM and gene stacking do not cause significantly unintended effects.

BackgroundGenetically modified (GM) soybeans provide a huge amount of food for human consumption and animal feed. However, the possibility of unexpected effects of transgenesis has increased food safety concerns. High-throughput sequencing profiling provides a powerful approach to directly evaluate unintended effects caused by foreign genes.ResultsIn this study, we performed transcriptomic analyses to evaluate differentially expressed genes (DEGs) in individual soybean tissues, including cotyledon (C), germ (G), hypocotyl (H), and radicle (R), instead of using the whole seed, from four GM and three non-GM soybean lines. A total of 3,351 DEGs were identified among the three non-GM soybean lines. When the GM lines were compared with their non-GM parents, 1,836 to 4,551 DEGs were identified. Furthermore, Gene Ontology (GO) analysis of the DEGs showed more abundant categories of GO items (199) among non-GM lines than between GM lines and the non-GM natural varieties (166). Results of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that most KEGG pathways were the same for the two types of comparisons.ConclusionsThe study successfully employed RNA sequencing to assess the differences in gene expression among four tissues of seven soybean varieties, and the results suggest that transgenes do not induce massive transcriptomic alterations in transgenic soybeans compared with those that exist among natural varieties. This work thus provides important support for safety evaluation of genetically modified soybeans based on seed tissues.

The transgenic rice G6H1 was a new event with the traits of herbicide-tolerance and insect-resistant. Herein, we developed one event-specific real-time PCR method with high specificity and sensitivity for G6H1 event quantitative analysis, and validated its performance on practical samples quantification through a collaborative ring trial. A total of eight laboratories participated in this validation and quantified three blind G6H1 powder samples including DNA extraction and real-time PCR analysis. The statistically analyzed results from returned data confirmed its high PCR efficiency and good linearity, trueness, and precision, indicating that the developed G6H1 real-time PCR assay was accurate, reliable, and comparable for G6H1 identification and quantification.

Mixed pixels universally exist in remote sensing images, and they are one of the main obstacles for further improving the accuracy of land cover recognition and classification. Since the concept of sub-pixel mapping (SPM) is proposed, SPM technology has rapidly become an important method to solve the problem of mixed pixels. To further improve SPM accuracy, this paper first proposes a double-calculated spatial attraction model (DSAM) combining the advantages of the spatial attraction model (SAM) and the pixel swap model (PSM). Then, based on the full validation of the proposed DSAM, how multiple factors affect the SPM accuracy is analyzed using the multispectral remote sensing (MRS) images. Finally, by analyzing the maximum variations in the ranges of the overall accuracy and the kappa coefficient under different multiple factors, the order of factors influencing SPM accuracy is determined as follows: reconstruction scale > image spatial resolution > pixel spatial relationships. The results can serve as a reference for other scholars in setting model parameters and selecting the appropriate remote sensing data, thereby helping them achieve more accurate SPM results.

The upper Carboniferous Batamayineishan mudstones are an important and effective gas source rock in the Wulungu area. These sediments are rich in organic matter, however, organic matter accumulation has not been studied before in these mudstones. The major and trace elements were used to reconstruct the depositional environments of these sediments and to improve our understanding of the factors controlling organic matter accumulation. Major and trace elements data indicate that: (1) paleoweathering was low to intermediate in the source terrain; (2) paleoclimate was hot and arid during late Carboniferous in the Wulungu area; (3) low paleoproductivity may have been induced by the low input of nutrients caused by the hot arid climate; (4) the Batamayineishan mudstones were deposited under a reducing environment; (5) organic matter accumulation in these studied deposits was mainly controlled by the input of higher plants rather than redox conditions and paleoproductivity.

Graphite plugged bronze has been primarily applied as the self-lubricating part in the tough oilless conditions, and understanding the detailed wear characteristics and the contacting stress evolution of graphite plugged bronze was important to improve its design for the in-service reliability. This study investigated the wear characteristics and contacting stress of graphite plugged bronze sliding plate from the field trial by means of the multiple topographic characterizations and computational analysis. The results revealed that abrasive wear and adhesive wear predominated on the contacting surface of graphite plugged bronze plate, accompanied by the localized fatigue and erosion. Computational simulation well illustrated the increasingly accumulated stress at the boundary between bronze and graphite as referenced with the stress evolution of bronze matrix and graphite plug, which was considered to be the leading cause of aggravated wear over time. Finding from this study provided the primary wear features of graphite plugged bronze component, which had potential application for the further optimization of the structural restoration and tribological issues of graphite plugged bronze.

Bacillus thuringiensis (Bt) can synthesize insecticides to efficiently control insects. In this study, Bt strain S3580-1 with mosquitocidal activity was subjected to whole genome sequencing using an Illumina HiSeq 2000 system. A novel toxin, Cry80Aa1, was identified based on the resulting data. A conserved domain analysis revealed that Cry80Aa1 includes the Ricin_B_lectin domain (located at 10–150) and the Toxin_10 domain (located at 155–353). Phylogenetic tree analysis showed that Cry80Aa1 was in a distinct clade significantly distinguished from the known Cry proteins containing the Toxin_10 domain. Bioassays demonstrated that the Cry80Aa1 protein exhibited toxicity to third instar larvae of Culex pipiens pallens (LC50: 71.9 μg/mL; 95% FL: 59.5–122.7 μg/mL).

Background Injection of adipose-derived stem cells (ASCs) is a promising treatment for facial contour deformities. However, its treatment mechanisms remain largely unknown. The study aimed to explain the molecular mechanisms of adipogenic differentiation from ASCs based on the roles of long noncoding RNAs (lncRNAs). Methods Datasets of mRNA–lncRNA (GSE113253) and miRNA (GSE72429) expression profiling were collected from Gene Expression Omnibus database. The differentially expressed genes (DEGs), lncRNAs (DELs) and miRNAs (DEMs) between undifferentiated and adipocyte differentiated human ASCs were identified using the Linear Models for Microarray Data method. DELs related co-expression and competing endogenous RNA (ceRNA) networks were constructed. Protein–protein interaction (PPI) analysis was performed to screen crucial target genes. Results A total of 748 DEGs, 17 DELs and 51 DEMs were identified. A total of 13 DELs and 279 DEGs with Pearson correlation coefficients > 0.9 and p-value < 0.01 were selected to construct the co-expression network. A total of 151 interaction pairs among 112 nodes (10 DEMs; eight DELs; 94 DEGs) were obtained to construct the ceRNA network. By comparing the lncRNAs and mRNAs in two networks, five lncRNAs (SNHG9, LINC02202, UBAC2-AS1, PTCSC3 and myocardial infarction associated transcript (MIAT)) and 32 genes (i.e., such as phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), protein tyrosine phosphatase receptor type B (PTPRB)) were found to be shared. PPI analysis demonstrated PIK3R1 , forkhead box O1 (FOXO1; a transcription factor) and estrogen receptor 1 (ESR1) were hub genes, which could be regulated by the miRNAs that interacted with the above five lncRNAs, such as LINC02202-miR-136-5p-PIK3R1, LINC02202-miR-381-3p-FOXO1 and MIAT-miR-18a-5p-ESR1. LINC02202 also could directly co-express with PIK3R1. Furthermore, PTPRB was predicted to be modulated by co-expression with LINC01119. Conclusion MIAT, LINC02202 and LINC01119 may be potentially important, new lncRNAs associated with adipogenic differentiation of ASCs. They may be involved in adipogenesis by acting as a ceRNA or co-expressing with their targets.

To investigate the unintended effects of genetically modified (GM) crops, an isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative proteomic analysis was performed with seed cotyledons of two GM soybean lines, MON87705 and MON87701×MON89788, and the corresponding non-transgenic isogenic variety A3525. Thirty-five differentially abundant proteins (DAPs) were identified in MON87705/A3525, 27 of which were upregulated and 8 downregulated. Thirty-eight DAPs were identified from the MON87701×MON89788/A3525 sample, including 29 upregulated proteins and 9 downregulated proteins. Pathway analysis showed that most of these DAPs participate in protein processing in endoplasmic reticulum and in metabolic pathways. Protein–protein interaction analysis of these DAPs demonstrated that the main interacting proteins are associated with post-translational modification, protein turnover, chaperones and signal transduction mechanisms. Nevertheless, these DAPs were not identified as new unintended toxins or allergens and only showed changes in abundance. All these results suggest that the seed cotyledon proteomic profiles of the two GM soybean lines studied were not dramatically altered compared with that of their natural isogenic control.

The accurate monitoring and quantification of genetically modified organisms (GMOs) are key points for the implementation of labeling regulations, and a certified reference material (CRM) acts as the scaleplate for quantifying the GM contents of foods/feeds and evaluating a GMO analytical method or equipment. Herein we developed a series of CRMs for transgenic rice event G6H1, which possesses insect-resistant and herbicide-tolerant traits. Three G6H1 CRMs were produced by mixing seed powders obtained from homozygous G6H1 and its recipient cultivar Xiushui 110 at mass ratios of 49.825%, 9.967%, and 4.986%. The between-bottle homogeneity and within-bottle homogeneity were thoroughly evaluated with consistent results. The potential DNA degradation in transportation and shelf life were evaluated with an expiration period of at least 12 months. The property values of three CRMs (G6H1a, G6H1b, G6H1c) were given as (49.825 ± 0.448) g/kg, (9.967 ± 1.757) g/kg, and (4.986 ± 1.274 g/kg based on mass fraction ratio,...

Glyphosate is one of the most commonly used broad-spectrum herbicides with little to no hazard to animals, human beings, or the environment. Some microbial 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase variants are not inhibited by glyphosate, and they provide a powerful tool to engineer glyphosate-tolerant plants. However, the unintended effects of EPSP synthase expression patterns on microbes are not yet clear. Here, we use an Affymetrix GeneChip analysis to study how introduction of a heterologous glyphosate-tolerant EPSP synthase into a model microorganism Escherichia coli (E. coli) affects the global gene expression profile. The profile showed that 161 of 4071 genes were differentially expressed after the introduction of the synthase: 19 (0.47%) were up-regulated and 143 (3.49%) were down-regulated. The microarray results, in combination with BiOLOG substrate utilization and amino acid composition assays, suggested that heterologous EPSP synthase expression had very minor effects on E. coli. Although a small number of genes and metabolites were affected by EPSP synthase expression, no functional correlations were identified among the dataset. This study may shed light on the effect of EPSP synthase expression on microbes, which should help in the assessment of environmental safety.

Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37–42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15–25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean). With this novel amplification method, the test time was significantly shortened and the reaction process was simplified, thus, this method represents an effective approach to the rapid detection of GM crops.

In this paper, we employed terahertz time domain spectroscopy (THz-TDS) to investigate the nitrate () concentration in four types of nitrate solution (sodium nitrate, aluminum nitrate, calcium nitrate and magnesium nitrate). Their absorption coefficient and refractive index were calculated in 0.2–2.5 THz, and a logarithmic relationship was observed between NO3− concentrations and selected optical parameters regardless of the kinds of nitrate solution. Partial least square (PLS) model was built between THz-TDS and NO3− concentration. The correlation coefficient of PLS model was calculated. The results make the quantitative analysis of NO3− concentration possible by THz-TDS and indicate the bright future in practical application.

A novel, Gram-stain-negative, aerobic, rod-shaped, non-motile and moderately halophilic bacterium, designated strain BJGMM-B45T, was isolated from a saline–alkali soil collected from Shandong Province, China. Growth of strain BJGMM-B45T occurred at 10–45 °C (optimum, 30 °C) and pH 5.0–12.0 (optimum, pH 7.0) on Luria–Bertani agar medium with 1–20 % (w/v) NaCl (optimum, 7–10 %). The predominant respiratory quinone was Q-9. The major cellular fatty acids (>5 %) were C18 : 1ω7c, C16 : 0, C19 : 0 cyclo ω8c, summed feature 3, C12 : 0 3-OH and C12 : 0. The genomic DNA G+C content was 57.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BJGMM-B45T belonged to the genus Halomonas in the class Gammaproteobacteria . The closest relatives were Halomonas cupida DSM 4740T (98.2 % 16S rRNA gene sequence similarity) and Halomonas denitrificans M29T (97.8 %). Levels of DNA–DNA relatedness between strain BJGMM-B45T and Halomonas cupida CGMCC 1.2312T and Halomonas denitrificans DSM 18045T were 57.0 and 58.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain BJGMM-B45T is considered to represent a novel species of the genus Halomonas , for which the name Halomonas huangheensis sp. nov. is proposed. The type strain is BJGMM-B45T ( = ACCC 05850T = KCTC 32409T).

This paper introduces the terahertz time-domain spectroscopy (THz-TDS) used for the quantitative detection of n-heptane volume ratios in 41 n-heptane and n-octane mixtures with the concentration range of 0–100% at the intervals of 2.5%. Among 41 samples, 33 were used for calibration and the remaining 8 for validation. Models of chemometrics methods, including partial least squares (PLS) and back propagation-artificial neural network (BP-ANN), were built between the THz-TDS and the n-heptane percentage. To evaluate the quality of the built models, we calculated the correlation coefficient (R) and root-mean-square errors (RMSE) of calibration and validation models. R and RMSE of two methods were close to 1 and 0 within acceptable levels, respectively, demonstrating that the combination of THz-TDS and chemometrics methods is a potential and promising tool for further quantitative detection of nalkanes.

Terahertz time-domain spectroscopy (THz-TDS) was used for the quantitative detection of sulfur content in gasoline. Models of chemo metrics methods and partial least squares (PLS) were built to measure THz-TDS and the sulfur content. All of the samples were divided into two parts. One part was used for calibration and the other one for validation. In order to evaluate the quality of the models, the correlation coefficient (R) and root-mean-square errors (RMSE) of calibration and validation models were calculated. The value of R and RMSE were close to 1 and 0 within acceptable levels, respectively, indicating that the combination of THz-TDS and PLS is a potential method for further quantitative detection.

GM crops detection commonly uses PCR method currently. It takes too long and needs thermal cycling instruments with accurate temperature control, so it is not suitable for field testing. In this study, event-specific detection method for transgenic insect resistance rice Kefeng 6 and its derivates based on real-time fluorescent recombinase ploymerase amplification (RPA) was established. According to the integration junction sequence of Kefeng 6, we designed and screened a set of RPA primers and probes combination which fit for RPA assays. The results showed that 500 copies of the target molecules in samples could be detected stablely and specifically by the method. The method can finish detection in 10 to 20 min, simplifying the test procedure by real-time fluorescence detection. Detection time was greatly shortened comparing with the conventional PCR detection which needed several hours. It has great application value for field transgenic detection using lithium battery-powered portable apparatus.

We have reported on the lateral photovoltaic effect of LaTiO3films epitaxially grown on (100) SrTiO3substrates. Under illumination of continuous 1064 nm laser beam on the LaTiO3film through SrTiO3substrate, the open-circuit photovoltage depended linearly on the illuminated position. The photosensitivity can be modified by bias current. These results indicated that the LaTiO3films give rise to a potentially photoelectronic device for near infrared position-sensitive detection.

Gene flow from genetically modified (GM) crops to the same species or wild relatives is a major concern in risk assessment. Transgenic rice with insect and/or disease resistance, herbicide, salt and/or drought tolerance and improved quality has been successfully developed. However, data on rice gene flow from environmental risk assessment studies are currently insufficient for the large-scale commercialization of GM rice. We have provided data on the gene flow frequency at 17 distances between a GM japonica line containing the bar gene as a pollen donor and two indica hybrid rice varieties and four male-sterile (ms) lines. The GM line was planted in a 640 m2 in an isolated experimental plot (2.4 ha), which simulates actual conditions of rice production with pollen competition. Results showed that: (1) under parallel plantation at the 0-m zone, the transgene flow frequency to the ms lines ranged from 3.145 to 36.116% and was significantly higher than that to hybrid rice cultivars (0.037-0.045%). (2) Gene flow frequency decreased as the distance increased, with a sharp cutoff point at about 1-2 m; (3) The maximum distance of transgene flow was 30-40 m to rice cultivars and 40-150 m to ms lines. We believe that these data will be useful for the risk assessment and management of transgenic rice lines, especially in Asia where 90% of world's rice is produced and hybrid rice varieties are extensively used.